About

MolView is an intuitive, Open-Source web-application to make science and education more awesome! MolView is mainly intended as web-based data visualization platform. You can use MolView to search through different scientific databases including compound databases, protein databases and spectral databases, and view records from these databases as interactive visualizations using WebGL and HTML5 technologies. This web application is built on top of the JavaScript libraries and online services listed below. The Virtual Model Kit has been a source of inspiration for the birth of this project.

Help

Click one of the subjects below to learn more. You can also watch some videos on YouTube to get started.

Subjects

Drawing structural formulas

MolView consists of two main parts, a structural formula editor and a 3D model viewer. The structural formula editor is surround by three toolbars which contain the tools you can use in the editor. Once you’ve drawn a molecule, you can click the 2D to 3D button to convert the molecule into a 3D model which is then displayed in the viewer. Below is a list of all sketch tools.

Top toolbar

Trash: clear the entire canvas

Eraser: erase atoms, bonds or the current selection

Undo/redo: undo or redo your recent changes

Selection tools: all these tool can be used to drag the current selection or individual atoms and bonds. You can add/remove atoms and bonds to the selection by clicking them. If you have selected a separate fragment, you can rotate it by dragging an atom in the selection. You can delete the selection using the DEL key or using the eraser tool. Each tool has different behavior for the right mouse button:

Drag: move the entire molecule (you can already use the left mouse button for this)

Rectangle select: select atoms and bonds using a rectangular selection area

Lasso select: select atoms and bonds by drawing a freehand selection area

Left toolbar

Fragments: pick one of the fragments (benzene, cyclopropane, etc.) and add fragments

Chain: create a chain of carbon atoms

Charge: increment (+) or decrement (-) the charge of atoms

Right toolbar

In this toolbar you can select from a number of elements, you can also pick an element from the periodic table using the last button. You can use the element to create new atoms or modify existing atoms.

Finding structures

You can load molecules from large databases like PubChem and RCSB using the search form located on the left side of the menu-bar. Just type what you are looking for and a list of available molecules will appear.

You can also click on the dropdown button next to the search field to select a specific database. This will perform a more extensive search on the selected database. Currently, three big databases are supported:

PubChem

The RCSB Protein Data Bank

The Crystallography Open Database

Tools

The Tools menu contains several utility functions which are listed below.

Link

You can embed or share a specific compound, macromolecule or crystal using the provided URL or HTML code. Note that the linked structure is the one which is currently displayed in the model window. You can also copy the URL from the address bar in order to link to the current structure.

Information card

Spectroscopy

This shows a new layer where you can view molecular spectra of the current structural formula (loaded from the Sketcher) More details are covered in the Spectroscopy chapter.

3D model resource

This redirects you to the web-page for the current 3D model on the website of its source database (except when the model is resolved using the Chemical Identifier Resolver)

Advanced search

These functions allow you to perform some advanced searches through the PubChem database using the structural formula from the sketcher.

Similarity search: search for compounds with a similar structural formula

Substructure search: search for compounds with the current structure as subset

Superstructure search: search for compounds with the current structure as superset

Spectroscopy

You can open the Spectroscopy view via Tools > Spectroscopy. You can view three kinds of molecular spectra.

Mass spectrum

IR spectrum

H1-NMR prediction

Export data

You can also export different kinds of data from the currently selected spectrum.

PNG image: snapshot from interactive spectrum

JCAMP file: JCAMP-DX file of the current spectrum

3D model

The Model menu contains some general functions for the 3D model.

Reset

This function sets the model position, zoom and rotation back to default.

Representation

You can choose from a list of different molecule representations including; ball and stick, stick, van der Waals spheres, wireframe and lines. Macromolecules are automatically drawn using ribbons.

Background

You can switch between a black, gray or white background. The default background is black (exported images from GLmol or ChemDoodle have a transparent background)

Engines

You can choose from three different render engines: GLmol, Jmol and ChemDoodle. GLmol is used as default render engine. GLmol and ChemDoodle are based on WebGL, a browser technology to support 3D graphics. If WebGL is not available in your browser, Jmol will be used for all rendering.

MolView automatically switches to:

Jmol if you execute functions from the Jmol menu

GLmol if you load macromolecules (due to significant higher performance)

You might want to switch back to GLmol when you do no longer need Jmol or ChemDoodle since GLmol has a better performance.

Note that macromolecules are drawn slightly different in each engine. ChemDoodle provides the finest display. You should, however, avoid using ChemDoodle for very large macromolecules.

Model transformation

You can rotate, pan and zoom the 3D model. Use the right button for rotation, the middle button for translation (except for ChemDoodle) and the scrollwheel for zooming. On touch devices, you can rotate the model with one finger and scale the model using two fingers.

Crystallography

You can load an array of crystal cells (2x2x2 or 1x3x3) or a single unit cell when viewing crystal structures.

Fog and clipping

When you are viewing large structures, like proteins, it can be useful to hide a certain part using fog or a clipping plane. GLmol offers a few options to do this.

Fog: you can move the fog forward by dragging the mouse up while holding CTRL + SHIFT (drag in the opposite direction to move the fog backward)

Clipping plane: you can move a frontal clipping plane into the structure by dragging the mouse to the left while holding CTRL + SHIFT (drag in the opposite direction to move the clipping plane back)

Protein display

The Protein menu offers a number of protein display settings including different color schemes and different chain representations.

Show bio assembly

When loading a protein structure, MolView shows the asymmetric unit by default. This function allows you to view the full biological unit instead.

Chain representation

You can choose from four different chain representations. You can also view the full chain structure by enabling the Bonds option.

Ribbon: draws ribbon diagram (default representation)

Cylinder and plate: solid cylinders for α-helices and solid plates for β-sheets